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Ramírez Martínez J, Guillou S, Le Prieur S, Di Vittorio P, Bonal F, Taliadoros D, Gueret E, Fournier E, Stukenbrock EH, Valade R, Gladieux P. Deep population structure linked to host vernalization requirement in the barley net blotch fungal pathogen. Microb Genom 2024; 10:001241. [PMID: 38713188 PMCID: PMC11170133 DOI: 10.1099/mgen.0.001241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 04/09/2024] [Indexed: 05/08/2024] Open
Abstract
Invasive fungal pathogens pose a substantial threat to widely cultivated crop species, owing to their capacity to adapt to new hosts and new environmental conditions. Gaining insights into the demographic history of these pathogens and unravelling the mechanisms driving coevolutionary processes are crucial for developing durably effective disease management programmes. Pyrenophora teres is a significant fungal pathogen of barley, consisting of two lineages, Ptt and Ptm, with global distributions and demographic histories reflecting barley domestication and spread. However, the factors influencing the population structure of P. teres remain poorly understood, despite the varietal and environmental heterogeneity of barley agrosystems. Here, we report on the population genomic structure of P. teres in France and globally. We used genotyping-by-sequencing to show that Ptt and Ptm can coexist in the same area in France, with Ptt predominating. Furthermore, we showed that differences in the vernalization requirement of barley varieties were associated with population differentiation within Ptt in France and at a global scale, with one population cluster found on spring barley and another population cluster found on winter barley. Our results demonstrate how cultivation conditions, possibly associated with genetic differences between host populations, can be associated with the maintenance of divergent invasive pathogen populations coexisting over large geographic areas. This study not only advances our understanding of the coevolutionary dynamics of the Pt-barley pathosystem but also prompts further research on the relative contributions of adaptation to the host versus adaptation to abiotic conditions in shaping Ptt populations.
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Affiliation(s)
- Julie Ramírez Martínez
- PHIM Plant Health Institute, Univ. Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Sonia Guillou
- PHIM Plant Health Institute, Univ. Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | | | - Pauline Di Vittorio
- PHIM Plant Health Institute, Univ. Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Florelle Bonal
- UMR AGAP (Amélioration génétique et adaptation des plantes), Montpellier, France
| | - Demetris Taliadoros
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany
- Christian-Albrechts University of Kiel, Am Botanischen Garten 9-11, 24118, Kiel, Germany
| | - Elise Gueret
- MGX-Montpellier GenomiX, University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Elisabeth Fournier
- PHIM Plant Health Institute, Univ. Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Eva H. Stukenbrock
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany
- Christian-Albrechts University of Kiel, Am Botanischen Garten 9-11, 24118, Kiel, Germany
| | | | - Pierre Gladieux
- PHIM Plant Health Institute, Univ. Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
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Ecological speciation of Japanese hedgehog mushroom: Hydnum subalpinum sp. nov. is distinguished from its sister species H. repando-orientale by means of integrative taxonomy. Mycol Prog 2022. [DOI: 10.1007/s11557-022-01844-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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3
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Characterization of Host-Specific Genes from Pine- and Grass-Associated Species of the Fusarium fujikuroi Species Complex. Pathogens 2022; 11:pathogens11080858. [PMID: 36014979 PMCID: PMC9415769 DOI: 10.3390/pathogens11080858] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/20/2022] [Accepted: 07/25/2022] [Indexed: 11/16/2022] Open
Abstract
The Fusarium fujikuroi species complex (FFSC) includes socioeconomically important pathogens that cause disease for numerous crops and synthesize a variety of secondary metabolites that can contaminate feedstocks and food. Here, we used comparative genomics to elucidate processes underlying the ability of pine-associated and grass-associated FFSC species to colonize tissues of their respective plant hosts. We characterized the identity, possible functions, evolutionary origins, and chromosomal positions of the host-range-associated genes encoded by the two groups of fungi. The 72 and 47 genes identified as unique to the respective genome groups were potentially involved in diverse processes, ranging from transcription, regulation, and substrate transport through to virulence/pathogenicity. Most genes arose early during the evolution of Fusarium/FFSC and were only subsequently retained in some lineages, while some had origins outside Fusarium. Although differences in the densities of these genes were especially noticeable on the conditionally dispensable chromosome of F. temperatum (representing the grass-associates) and F. circinatum (representing the pine-associates), the host-range-associated genes tended to be located towards the subtelomeric regions of chromosomes. Taken together, these results demonstrate that multiple mechanisms drive the emergence of genes in the grass- and pine-associated FFSC taxa examined. It also highlighted the diversity of the molecular processes potentially underlying niche-specificity in these and other Fusarium species.
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Caffier V, Shiller J, Bellanger MN, Collemare J, Expert P, Gladieux P, Pascouau C, Sannier M, Le Cam B. Hybridizations Between formae speciales of Venturia inaequalis Pave the Way for a New Biocontrol Strategy to Manage Fungal Plant Pathogens. PHYTOPATHOLOGY 2022; 112:1401-1405. [PMID: 35080437 DOI: 10.1094/phyto-05-21-0222-sc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Hybridization and adaptation to new hosts are important mechanisms of fungal disease emergence. Evaluating the risk of emergence of hybrids with enhanced virulence is then key to develop sustainable crop disease management. We evaluated this risk in Venturia inaequalis, the fungus responsible for the common and serious scab disease on Rosaceae hosts, including apple, pyracantha, and loquat. Field isolates from these three hosts and progenies obtained from five crosses between formae speciales isolates collected from pyracantha (f. sp. pyracantha) and apple (f. sp. pomi) were tested for their pathogenicity on the three hosts. We confirmed a strict host specificity between isolates from apple and pyracantha and showed that most isolates were able to cause disease on loquat. None of the 251 progeny obtained from five crosses between V. inaequalis f. sp. pyracantha and V. inaequalis f. sp. pomi could infect apple. If confirmed on more crosses, the inability of the hybrids to infect apple could lead to a novel biocontrol strategy based on a sexual hijacking of V. inaequalis f. sp. pomi by a massive introduction of V. inaequalis f. sp. pyracantha in apple orchards. This strategy, analogous to the sterile insect approach, could lead to the collapse of the population size of V. inaequalis and dramatically reduce the use of chemicals in orchards.
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Affiliation(s)
- Valérie Caffier
- Univ Angers, Institut Agro, INRAE IRHS, SFR QUASAV, F-49000 Angers, France
| | - Jason Shiller
- Univ Angers, Institut Agro, INRAE IRHS, SFR QUASAV, F-49000 Angers, France
| | | | - Jérôme Collemare
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, Netherlands
| | - Pascale Expert
- Univ Angers, Institut Agro, INRAE IRHS, SFR QUASAV, F-49000 Angers, France
| | - Pierre Gladieux
- PHIM Plant Health Institute, Université Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Claire Pascouau
- Univ Angers, Institut Agro, INRAE IRHS, SFR QUASAV, F-49000 Angers, France
| | - Mélanie Sannier
- Univ Angers, Institut Agro, INRAE IRHS, SFR QUASAV, F-49000 Angers, France
| | - Bruno Le Cam
- Univ Angers, Institut Agro, INRAE IRHS, SFR QUASAV, F-49000 Angers, France
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Sugawara R, Maekawa N, Sotome K, Nakagiri A, Endo N. Systematic revision of Hydnum species in Japan. Mycologia 2022; 114:413-452. [PMID: 35394899 DOI: 10.1080/00275514.2021.2024407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Hydnum (Hydnaceae, Basidiomycota) exhibits endemic species diversity in East Asia; however, few comprehensive systematic studies have been conducted to date. Here, we performed morphological, ecological, phylogenetic, and biological evaluations of the taxonomy of Hydnum species in Japan. In total, 186 Japanese Hydnum specimens were used for morphological observations. Phylogenetic trees were constructed using sequence data of nuc rDNA internal transcribed spacer ITS1-5.8S-ITS2 (ITS) region and a portion of translation elongation factor 1-α (tef1). Intra- and interspecific mating tests using 78 monokaryotic strains of 13 species did not conflict with species delimitation inferred from their ITS and tef1 phylogenetic relationships. This study provides detailed morphological descriptions of 15 rigorously identified species from Japan, nine of which are described as new: H. alboluteum, H. albopallidum, H. pinicola, H. itachiharitake, H. minospororufescens, H. orientalbidum, H. subberkeleyanum, H. tomaense, and H. tottoriense. Three species documented in this work are new to Japan: H. boreorepandum, H. mulsicolor, and H. umbilicatum. The remaining three species (H. cremeoalbum, H. minus, and H. repando-orientale), previously reported from Japan, are redescribed using data from newly collected materials. We also transferred two old species (Hericium fimbrillatum and Sarcodon nauseofoetidus) from East Asian Hydnum into other genera.
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Affiliation(s)
- Ryo Sugawara
- The United Graduate School of Agricultural Sciences, Tottori University, 4-101, Koyama, Tottori 680-8553, Japan
| | - Nitaro Maekawa
- Fungus/Mushroom Resource and Research Center, Faculty of Agriculture, Tottori University, 4-101, Koyama, Tottori 680-8553, Japan
| | - Kozue Sotome
- Fungus/Mushroom Resource and Research Center, Faculty of Agriculture, Tottori University, 4-101, Koyama, Tottori 680-8553, Japan
| | - Akira Nakagiri
- Fungus/Mushroom Resource and Research Center, Faculty of Agriculture, Tottori University, 4-101, Koyama, Tottori 680-8553, Japan
| | - Naoki Endo
- Fungus/Mushroom Resource and Research Center, Faculty of Agriculture, Tottori University, 4-101, Koyama, Tottori 680-8553, Japan
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Interspecific hybridization as a driver of fungal evolution and adaptation. Nat Rev Microbiol 2021; 19:485-500. [PMID: 33767366 DOI: 10.1038/s41579-021-00537-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/22/2021] [Indexed: 02/01/2023]
Abstract
Cross-species gene transfer is often associated with bacteria, which have evolved several mechanisms that facilitate horizontal DNA exchange. However, the increased availability of whole-genome sequences has revealed that fungal species also exchange DNA, leading to intertwined lineages, blurred species boundaries or even novel species. In contrast to prokaryotes, fungal DNA exchange originates from interspecific hybridization, where two genomes are merged into a single, often highly unstable, polyploid genome that evolves rapidly into stabler derivatives. The resulting hybrids can display novel combinations of genetic and phenotypic variation that enhance fitness and allow colonization of new niches. Interspecific hybridization led to the emergence of important pathogens of humans and plants (for example, various Candida and 'powdery mildew' species, respectively) and industrially important yeasts, such as Saccharomyces hybrids that are important in the production of cold-fermented lagers or cold-cellared Belgian ales. In this Review, we discuss the genetic processes and evolutionary implications of fungal interspecific hybridization and highlight some of the best-studied examples. In addition, we explain how hybrids can be used to study molecular mechanisms underlying evolution, adaptation and speciation, and serve as a route towards development of new variants for industrial applications.
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Sillo F, Garbelotto M, Giordano L, Gonthier P. Genic introgression from an invasive exotic fungal forest pathogen increases the establishment potential of a sibling native pathogen. NEOBIOTA 2021. [DOI: 10.3897/neobiota.65.64031] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Significant hybridization between the invasive North American fungal plant pathogen Heterobasidion irregulare and its Eurasian sister species H. annosum is ongoing in Italy. Whole genomes of nine natural hybrids were sequenced, assembled and compared with those of three genotypes each of the two parental species. Genetic relationships among hybrids and their level of admixture were determined. A multi-approach pipeline was used to assign introgressed genomic blocks to each of the two species. Alleles that introgressed from H. irregulare to H. annosum were associated with pathways putatively related to saprobic processes, while alleles that introgressed from the native to the invasive species were mainly linked to gene regulation. There was no overlap of allele categories introgressed in the two directions. Phenotypic experiments documented a fitness increase in H. annosum genotypes characterized by introgression of alleles from the invasive species, supporting the hypothesis that hybridization results in putatively adaptive introgression. Conversely, introgression from the native into the exotic species appeared to be driven by selection on genes favoring genome stability. Since the introgression of specific alleles from the exotic H. irregulare into the native H. annosum increased the invasiveness of the latter species, we propose that two invasions may be co-occurring: the first one by genotypes of the exotic species, and the second one by alleles belonging to the exotic species. Given that H. irregulare represents a threat to European forests, monitoring programs need to track not only exotic genotypes in native forest stands, but also exotic alleles introgressed in native genotypes.
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Hernández-Hernández T, Miller EC, Román-Palacios C, Wiens JJ. Speciation across the Tree of Life. Biol Rev Camb Philos Soc 2021; 96:1205-1242. [PMID: 33768723 DOI: 10.1111/brv.12698] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 02/13/2021] [Accepted: 02/16/2021] [Indexed: 01/04/2023]
Abstract
Much of what we know about speciation comes from detailed studies of well-known model systems. Although there have been several important syntheses on speciation, few (if any) have explicitly compared speciation among major groups across the Tree of Life. Here, we synthesize and compare what is known about key aspects of speciation across taxa, including bacteria, protists, fungi, plants, and major animal groups. We focus on three main questions. Is allopatric speciation predominant across groups? How common is ecological divergence of sister species (a requirement for ecological speciation), and on what niche axes do species diverge in each group? What are the reproductive isolating barriers in each group? Our review suggests the following patterns. (i) Based on our survey and projected species numbers, the most frequent speciation process across the Tree of Life may be co-speciation between endosymbiotic bacteria and their insect hosts. (ii) Allopatric speciation appears to be present in all major groups, and may be the most common mode in both animals and plants, based on non-overlapping ranges of sister species. (iii) Full sympatry of sister species is also widespread, and may be more common in fungi than allopatry. (iv) Full sympatry of sister species is more common in some marine animals than in terrestrial and freshwater ones. (v) Ecological divergence of sister species is widespread in all groups, including ~70% of surveyed species pairs of plants and insects. (vi) Major axes of ecological divergence involve species interactions (e.g. host-switching) and habitat divergence. (vii) Prezygotic isolation appears to be generally more widespread and important than postzygotic isolation. (viii) Rates of diversification (and presumably speciation) are strikingly different across groups, with the fastest rates in plants, and successively slower rates in animals, fungi, and protists, with the slowest rates in prokaryotes. Overall, our study represents an initial step towards understanding general patterns in speciation across all organisms.
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Affiliation(s)
- Tania Hernández-Hernández
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A.,Catedrática CONACYT asignada a LANGEBIO-UGA Cinvestav, Libramiento Norte Carretera León Km 9.6, 36821, Irapuato, Guanajuato, Mexico
| | - Elizabeth C Miller
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A
| | - Cristian Román-Palacios
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A
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Hessenauer P, Feau N, Gill U, Schwessinger B, Brar GS, Hamelin RC. Evolution and Adaptation of Forest and Crop Pathogens in the Anthropocene. PHYTOPATHOLOGY 2021; 111:49-67. [PMID: 33200962 DOI: 10.1094/phyto-08-20-0358-fi] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Anthropocene marks the era when human activity is making a significant impact on earth, its ecological and biogeographical systems. The domestication and intensification of agricultural and forest production systems have had a large impact on plant and tree health. Some pathogens benefitted from these human activities and have evolved and adapted in response to the expansion of crop and forest systems, resulting in global outbreaks. Global pathogen genomics data including population genomics and high-quality reference assemblies are crucial for understanding the evolution and adaptation of pathogens. Crops and forest trees have remarkably different characteristics, such as reproductive time and the level of domestication. They also have different production systems for disease management with more intensive management in crops than forest trees. By comparing and contrasting results from pathogen population genomic studies done on widely different agricultural and forest production systems, we can improve our understanding of pathogen evolution and adaptation to different selection pressures. We find that in spite of these differences, similar processes such as hybridization, host jumps, selection, specialization, and clonal expansion are shaping the pathogen populations in both crops and forest trees. We propose some solutions to reduce these impacts and lower the probability of global pathogen outbreaks so that we can envision better management strategies to sustain global food production as well as ecosystem services.
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Affiliation(s)
- Pauline Hessenauer
- Faculty of Forestry, Geography and Geomatics, Laval University, Quebec City, QC, G1V 0A6 Canada
| | - Nicolas Feau
- Faculty of Forestry, The University of British Columbia, Vancouver, BC, V6T 1Z4 Canada
| | - Upinder Gill
- College of Agriculture, Food Systems, and Natural Resources, North Dakota State University, Fargo, ND 58102, U.S.A
| | - Benjamin Schwessinger
- Research School of Biology, Australian National University, Acton, ACT 2601 Australia
| | - Gurcharn S Brar
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, V6T 1Z4 Canada
| | - Richard C Hamelin
- Faculty of Forestry, Geography and Geomatics, Laval University, Quebec City, QC, G1V 0A6 Canada
- Faculty of Forestry, The University of British Columbia, Vancouver, BC, V6T 1Z4 Canada
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Domestication of the Emblematic White Cheese-Making Fungus Penicillium camemberti and Its Diversification into Two Varieties. Curr Biol 2020; 30:4441-4453.e4. [PMID: 32976806 DOI: 10.1016/j.cub.2020.08.082] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 07/02/2020] [Accepted: 08/24/2020] [Indexed: 12/24/2022]
Abstract
Domestication involves recent adaptation under strong human selection and rapid diversification and therefore constitutes a good model for studies of these processes. We studied the domestication of the emblematic white mold Penicillium camemberti, used for the maturation of soft cheeses, such as Camembert and Brie, about which surprisingly little was known, despite its economic and cultural importance. Whole-genome-based analyses of genetic relationships and diversity revealed that an ancient domestication event led to the emergence of the gray-green P. biforme mold used in cheese making, by divergence from the blue-green wild P. fuscoglaucum fungus. Another much more recent domestication event led to the generation of the P. camemberti clonal lineage as a sister group to P. biforme. Penicillium biforme displayed signs of phenotypic adaptation to cheese making relative to P. fuscoglaucum, in terms of whiter color, faster growth on cheese medium under cave conditions, lower amounts of toxin production, and greater ability to prevent the growth of other fungi. The P. camemberti lineage displayed even stronger signs of domestication for all these phenotypic features. We also identified two differentiated P. camemberti varieties, apparently associated with different kinds of cheeses and with contrasted phenotypic features in terms of color, growth, toxin production, and competitive ability. We have thus identified footprints of domestication in these fungi, with genetic differentiation between cheese and wild populations, bottlenecks, and specific phenotypic traits beneficial for cheese making. This study has not only fundamental implications for our understanding of domestication but can also have important effects on cheese making.
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Van Wyk S, Wingfield BD, De Vos L, Santana QC, Van der Merwe NA, Steenkamp ET. Multiple independent origins for a subtelomeric locus associated with growth rate in Fusarium circinatum. IMA Fungus 2018; 9:27-36. [PMID: 30018870 PMCID: PMC6048564 DOI: 10.5598/imafungus.2018.09.01.03] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 02/19/2018] [Indexed: 12/28/2022] Open
Abstract
Fusarium is a diverse assemblage that includes a large number of species of considerable medical and agricultural importance. Not surprisingly, whole genome sequences for many Fusarium species have been published or are in the process of being determined, the availability of which is invaluable for deciphering the genetic basis of key phenotypic traits. Here we investigated the distribution, genic composition, and evolutionary history of a locus potentially determining growth rate in the pitch canker pathogen F. circinatum. We found that the genomic region underlying this locus is highly conserved amongst F. circinatum and its close relatives, except for the presence of a 12 000 base pair insertion in all of the examined isolates of F. circinatum. This insertion encodes for five genes and our phylogenetic analyses revealed that each was most likely acquired through horizontal gene transfer from polyphyletic origins. Our data further showed that this region is located in a region low in G+C content and enriched for repetitive sequences and transposable elements, which is situated near the telomere of Chromosome 3 of F. circinatum. As have been shown for other fungi, these findings thus suggest that the emergence of the unique 12 000 bp region in F. circinatum is linked to the dynamic evolutionary processes associated with subtelomeres that, in turn, have been implicated in the ecological adaptation of fungal pathogens.
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Affiliation(s)
- Stephanie Van Wyk
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
| | - Brenda D Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
| | - Lieschen De Vos
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
| | - Quentin C Santana
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
| | - Nicolaas A Van der Merwe
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
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Christie K, Strauss SY. Along the speciation continuum: Quantifying intrinsic and extrinsic isolating barriers across five million years of evolutionary divergence in California jewelflowers. Evolution 2018; 72:1063-1079. [DOI: 10.1111/evo.13477] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Accepted: 02/27/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Kyle Christie
- Department of Evolution and Ecology and Center for Population Biology University of California One Shields Avenue Davis California 95616
| | - Sharon Y. Strauss
- Department of Evolution and Ecology and Center for Population Biology University of California One Shields Avenue Davis California 95616
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13
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Hamberg L, de la Bastide P, Hintz W, Shamoun SF, Brandtberg M, Hantula J. Interfertility and genetic variability among European and North American isolates of the basidiomycete fungus Chondrostereum purpureum. Fungal Biol 2018; 122:659-667. [PMID: 29880201 DOI: 10.1016/j.funbio.2018.03.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 03/09/2018] [Accepted: 03/20/2018] [Indexed: 01/10/2023]
Abstract
The conspecificity of Finnish and western Canadian isolates of the decay fungus Chondrostereum purpureum was investigated by several approaches, including the assessment of genetic variability, mating and progeny analysis, and the analysis of selected phenotypic traits. Eight second-generation single spore strains per fungal isolate pairing were investigated with specific genetic markers developed for both Finnish and Canadian parental isolates. Tests of linkage disequilibrium were used to analyze whether these markers assorted independently among single spore strains. This procedure was similarly applied to the third-generation spore progeny. Finally, global non-metric multidimensional scaling was used to analyze independent random amplified microsatellite marker data to assess the genetic variability of the parental Finnish and Canadian isolates, and their second- and third-generation progeny. Our results revealed that the parental isolates from Finland and western Canada were genetically divergent, but no interfertility barriers were identified between these geographically distant fungi. Furthermore, parental genetic markers used in mating studies demonstrated that second- and third-generation spore progenies underwent normal meiosis and genetic recombination without linkage disequilibrium. Based on this work, the studied C. purpureum isolates from Finland and Canada can be considered as belonging to a single biological species, although genetic and limited phenotypic differentiation was observed.
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Affiliation(s)
- Leena Hamberg
- Natural Resources Institute Finland, P.O. Box 2 (Latokartanonkaari 9), FI-00790, Helsinki, Finland.
| | - Paul de la Bastide
- Department of Biology, Centre for Forest Biology, University of Victoria, P.O. Box 1700, STN CSC, Victoria, BC, V8W 2Y2, Canada.
| | - Will Hintz
- Department of Biology, Centre for Forest Biology, University of Victoria, P.O. Box 1700, STN CSC, Victoria, BC, V8W 2Y2, Canada.
| | - Simon Francis Shamoun
- Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre, 506 West Burnside Road, Victoria, BC, V8Z 1M5, Canada.
| | - Marina Brandtberg
- Verdera Ltd., P.O. Box 5, Kurjenkellontie 5 B, FI-02270, Espoo, Finland.
| | - Jarkko Hantula
- Natural Resources Institute Finland, P.O. Box 2 (Latokartanonkaari 9), FI-00790, Helsinki, Finland.
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14
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Devier B, Aguileta G, Hood ME, Giraud T. Using phylogenies of pheromone receptor genes in theMicrobotryum violaceumspecies complex to investigate possible speciation by hybridization. Mycologia 2017; 102:689-96. [DOI: 10.3852/09-192] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | - Gabriela Aguileta
- Ecologie, Systématique et Evolution, Université Paris-Sud, F-91405 Orsay cedex, France; CNRS F-91405 Orsay cedex, France
| | - Michael E. Hood
- Department of Biology, McGuire Life Sciences Building, Amherst College, Amherst, Massachusetts 01002-5000
| | - Tatiana Giraud
- Ecologie, Systématique et Evolution, Université Paris-Sud, F-91405 Orsay cedex, France; CNRS F-91405 Orsay cedex, France
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15
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Haight JE, Laursen GA, Glaeser JA, Taylor DL. Phylogeny of Fomitopsis pinicola: a species complex. Mycologia 2017; 108:925-938. [DOI: 10.3852/14-225r1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 06/21/2016] [Indexed: 11/10/2022]
Affiliation(s)
- John-Erich Haight
- Institute of Arctic Biology and the Biology and Wildlife Department, University of Alaska, Fairbanks, Alaska 99775
- USDA-FS Northern Research Station, One Gifford Pinchot Drive, Madison, Wisconsin 53726
| | - Gary A. Laursen
- Institute of Arctic Biology and the Biology and Wildlife Department, University of Alaska, Fairbanks, Alaska 99775
| | - Jessie A. Glaeser
- USDA-FS Northern Research Station, One Gifford Pinchot Drive, Madison, Wisconsin 53726
| | - D. Lee Taylor
- Institute of Arctic Biology and the Biology and Wildlife Department, University of Alaska, Fairbanks, Alaska 99775
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16
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The famous cultivated mushroom Bailinggu is a separate species of the Pleurotus eryngii species complex. Sci Rep 2016; 6:33066. [PMID: 27629112 PMCID: PMC5024158 DOI: 10.1038/srep33066] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 08/21/2016] [Indexed: 12/02/2022] Open
Abstract
The mushroom of the genus Pleurotus in western China, called Bailinggu, is a precious edible fungus with high economic value. However, its taxonomical position is unclear. Some researchers regard it as a variety of P. eryngii, namely P. eryngii var. tuoliensis, whereas others consider it to be a subspecies of P. eryngii, viz. P. eryngii subsp. tuoliensis. A total of 51 samples representing seven genetic groups of the genus Pleurotus were subjected to a phylogenetic analysis of partial sequences of the translation elongation factor 1 alpha gene (ef1a), the RNA polymerase II largest subunit gene (rpb1), the RNA polymerase II second largest subunit gene (rpb2) and nuc rDNA internal transcribed spacers (ITS). Our data indicate that the mushroom Bailinggu is a lineage independent of P. eryngii and should be lifted as its own species, namely P. tuoliensis. In addition, its known distribution range consists of both western China and Iran.
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17
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Ropars J, Lo YC, Dumas E, Snirc A, Begerow D, Rollnik T, Lacoste S, Dupont J, Giraud T, López-Villavicencio M. Fertility depression among cheese-making Penicillium roqueforti strains suggests degeneration during domestication. Evolution 2016; 70:2099-109. [PMID: 27470007 PMCID: PMC5129480 DOI: 10.1111/evo.13015] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 06/20/2016] [Accepted: 07/09/2016] [Indexed: 11/28/2022]
Abstract
Genetic differentiation occurs when gene flow is prevented, due to reproductive barriers or asexuality. Investigating the early barriers to gene flow is important for understanding the process of speciation. Here, we therefore investigated reproductive isolation between different genetic clusters of the fungus Penicillium roqueforti, used for maturing blue cheeses, and also occurring as food spoiler or in silage. We investigated premating and postmating fertility between and within three genetic clusters (two from cheese and one from other substrates), and we observed sexual structures under scanning electron microscopy. All intercluster types of crosses showed some fertility, suggesting that no intersterility has evolved between domesticated and wild populations despite adaptation to different environments and lack of gene flow. However, much lower fertility was found in crosses within the cheese clusters than within the noncheese cluster, suggesting reduced fertility of cheese strains, which may constitute a barrier to gene flow. Such degeneration may be due to bottlenecks during domestication and/or to the exclusive clonal replication of the strains in industry. This study shows that degeneration has occurred rapidly and independently in two lineages of a domesticated species. Altogether, these results inform on the processes and tempo of degeneration and speciation.
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Affiliation(s)
- Jeanne Ropars
- Origine, Structure, Evolution de la Biodiversité, UMR 7205 CNRS-MNHN, Muséum National d'Histoire Naturelle, CP39, 57 rue Cuvier, 75231, Paris Cedex 05, France.,Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, F-91405, Orsay cedex, France
| | - Ying-Chu Lo
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, F-91405, Orsay cedex, France
| | - Emilie Dumas
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, F-91405, Orsay cedex, France
| | - Alodie Snirc
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, F-91405, Orsay cedex, France
| | - Dominik Begerow
- Ruhr-Universität Bochum, AG Geobotanik Gebäude ND 03/174 Universitätsstraße 150 44780 Bochum, Germany
| | - Tanja Rollnik
- Ruhr-Universität Bochum, AG Geobotanik Gebäude ND 03/174 Universitätsstraße 150 44780 Bochum, Germany
| | - Sandrine Lacoste
- Origine, Structure, Evolution de la Biodiversité, UMR 7205 CNRS-MNHN, Muséum National d'Histoire Naturelle, CP39, 57 rue Cuvier, 75231, Paris Cedex 05, France
| | - Joëlle Dupont
- Origine, Structure, Evolution de la Biodiversité, UMR 7205 CNRS-MNHN, Muséum National d'Histoire Naturelle, CP39, 57 rue Cuvier, 75231, Paris Cedex 05, France
| | - Tatiana Giraud
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, F-91405, Orsay cedex, France
| | - Manuela López-Villavicencio
- Origine, Structure, Evolution de la Biodiversité, UMR 7205 CNRS-MNHN, Muséum National d'Histoire Naturelle, CP39, 57 rue Cuvier, 75231, Paris Cedex 05, France.
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18
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Du XH, Zhao Q, Xu J, Yang ZL. High inbreeding, limited recombination and divergent evolutionary patterns between two sympatric morel species in China. Sci Rep 2016; 6:22434. [PMID: 26928176 PMCID: PMC4772476 DOI: 10.1038/srep22434] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 02/08/2016] [Indexed: 12/20/2022] Open
Abstract
As highly prized, popular mushrooms, morels are widely distributed in the northern hemisphere, with China as a modern centre of speciation and diversity. Overharvesting of morels has caused concern over how to effectively preserve their biological and genetic diversity. However, little is known about their population biology and life cycle. In this study, we selected two sympatric phylogenetic species, Mel-13 (124 collections from 11 geographical locations) and Morchella eohespera (156 collections from 14 geographical locations), using fragments of 4 DNA sequences, to analyse their genetic structure. Our results indicated significant differentiation among geographic locations in both species, whereas no obvious correlation between genetic and geographic distance was identified in either species. M. eohespera exhibited a predominantly clonal population structure with limited recombination detected in only 1 of the 14 geographic locations. In contrast, relatively frequent recombination was identified in 6 of the 11 geographic locations of Mel-13. Our analysis indicated that the sympatric species Mel-13 and M. eohespera might have divergent evolutionary patterns, with the former showing signatures of recent population expansion and the latter being relatively stable. Interestingly, we found no heterozygosity but strong evidence for genealogical incongruence, indicating a high level of inbreeding and hybridisation among morel species.
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Affiliation(s)
- Xi-Hui Du
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Qi Zhao
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Zhu L Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
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19
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Gladieux P, Wilson BA, Perraudeau F, Montoya LA, Kowbel D, Hann-Soden C, Fischer M, Sylvain I, Jacobson DJ, Taylor JW. Genomic sequencing reveals historical, demographic and selective factors associated with the diversification of the fire-associated fungus Neurospora discreta. Mol Ecol 2015; 24:5657-75. [PMID: 26453896 DOI: 10.1111/mec.13417] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 10/05/2015] [Accepted: 10/06/2015] [Indexed: 12/30/2022]
Abstract
Delineating microbial populations, discovering ecologically relevant phenotypes and identifying migrants, hybrids or admixed individuals have long proved notoriously difficult, thereby limiting our understanding of the evolutionary forces at play during the diversification of microbial species. However, recent advances in sequencing and computational methods have enabled an unbiased approach whereby incipient species and the genetic correlates of speciation can be identified by examining patterns of genomic variation within and between lineages. We present here a population genomic study of a phylogenetic species in the Neurospora discreta species complex, based on the resequencing of full genomes (~37 Mb) for 52 fungal isolates from nine sites in three continents. Population structure analyses revealed two distinct lineages in South-East Asia, and three lineages in North America/Europe with a broad longitudinal and latitudinal range and limited admixture between lineages. Genome scans for selective sweeps and comparisons of the genomic landscapes of diversity and recombination provided no support for a role of selection at linked sites on genomic heterogeneity in levels of divergence between lineages. However, demographic inference indicated that the observed genomic heterogeneity in divergence was generated by varying rates of gene flow between lineages following a period of isolation. Many putative cases of exchange of genetic material between phylogenetically divergent fungal lineages have been discovered, and our work highlights the quantitative importance of genetic exchanges between more closely related taxa to the evolution of fungal genomes. Our study also supports the role of allopatric isolation as a driver of diversification in saprobic microbes.
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Affiliation(s)
- Pierre Gladieux
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.,Ecologie Systematique Evolution, Université Paris Sud, Batiment 360, 91405, Orsay, France
| | | | - Fanny Perraudeau
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.,Ecole Polytechnique, Route de Saclay, 91128, Palaiseau, France
| | - Liliam A Montoya
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - David Kowbel
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | | | - Monika Fischer
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Iman Sylvain
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - David J Jacobson
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - John W Taylor
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
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20
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Bacquet PMB, Brattström O, Wang HL, Allen CE, Löfstedt C, Brakefield PM, Nieberding CM. Selection on male sex pheromone composition contributes to butterfly reproductive isolation. Proc Biol Sci 2015; 282:20142734. [PMID: 25740889 DOI: 10.1098/rspb.2014.2734] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Selection can facilitate diversification by inducing character displacement in mate choice traits that reduce the probability of maladaptive mating between lineages. Although reproductive character displacement (RCD) has been demonstrated in two-taxa case studies, the frequency of this process in nature is still debated. Moreover, studies have focused primarily on visual and acoustic traits, despite the fact that chemical communication is probably the most common means of species recognition. Here, we showed in a large, mostly sympatric, butterfly genus, a strong pattern of recurrent RCD for predicted male sex pheromone composition, but not for visual mate choice traits. Our results suggest that RCD is not anecdotal, and that selection for divergence in male sex pheromone composition contributed to reproductive isolation within the Bicyclus genus. We propose that selection may target olfactory mate choice traits as a more common sensory modality to ensure reproductive isolation among diverging lineages than previously envisaged.
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Affiliation(s)
- P M B Bacquet
- Evolutionary Ecology and Genetics Group, Biodiversity Research Centre, Earth and Life Institute, Université Catholique de Louvain, Croix du Sud 4-5, 1348 Louvain-la-Neuve, Belgium
| | - O Brattström
- Department of Zoology, University Museum of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - H-L Wang
- Department of Biology, Pheromone Group, Lund University, SE-223 62 Lund, Sweden
| | - C E Allen
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - C Löfstedt
- Department of Biology, Pheromone Group, Lund University, SE-223 62 Lund, Sweden
| | - P M Brakefield
- Department of Zoology, University Museum of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - C M Nieberding
- Evolutionary Ecology and Genetics Group, Biodiversity Research Centre, Earth and Life Institute, Université Catholique de Louvain, Croix du Sud 4-5, 1348 Louvain-la-Neuve, Belgium
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21
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Ropars J, Rodríguez de la Vega RC, López-Villavicencio M, Gouzy J, Sallet E, Dumas É, Lacoste S, Debuchy R, Dupont J, Branca A, Giraud T. Adaptive Horizontal Gene Transfers between Multiple Cheese-Associated Fungi. Curr Biol 2015; 25:2562-9. [PMID: 26412136 PMCID: PMC4598740 DOI: 10.1016/j.cub.2015.08.025] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 07/09/2015] [Accepted: 08/11/2015] [Indexed: 11/29/2022]
Abstract
Domestication is an excellent model for studies of adaptation because it involves recent and strong selection on a few, identified traits [1–5]. Few studies have focused on the domestication of fungi, with notable exceptions [6–11], despite their importance to bioindustry [12] and to a general understanding of adaptation in eukaryotes [5]. Penicillium fungi are ubiquitous molds among which two distantly related species have been independently selected for cheese making—P. roqueforti for blue cheeses like Roquefort and P. camemberti for soft cheeses like Camembert. The selected traits include morphology, aromatic profile, lipolytic and proteolytic activities, and ability to grow at low temperatures, in a matrix containing bacterial and fungal competitors [13–15]. By comparing the genomes of ten Penicillium species, we show that adaptation to cheese was associated with multiple recent horizontal transfers of large genomic regions carrying crucial metabolic genes. We identified seven horizontally transferred regions (HTRs) spanning more than 10 kb each, flanked by specific transposable elements, and displaying nearly 100% identity between distant Penicillium species. Two HTRs carried genes with functions involved in the utilization of cheese nutrients or competition and were found nearly identical in multiple strains and species of cheese-associated Penicillium fungi, indicating recent selective sweeps; they were experimentally associated with faster growth and greater competitiveness on cheese and contained genes highly expressed in the early stage of cheese maturation. These findings have industrial and food safety implications and improve our understanding of the processes of adaptation to rapid environmental changes. New HTRs are found in cheese fungi HTRs are flanked by specific transposable elements HTRs have spread in cheese-associated fungi through recent selective sweeps Experiments link two HTRs to growth and competitive advantages on cheese
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Affiliation(s)
- Jeanne Ropars
- Ecologie, Systématique et Evolution, UMR8079, Univ. Paris-Sud, 91405 Orsay, France; Ecologie, Systématique et Evolution, UMR8079, CNRS, 91405 Orsay, France
| | - Ricardo C Rodríguez de la Vega
- Ecologie, Systématique et Evolution, UMR8079, Univ. Paris-Sud, 91405 Orsay, France; Ecologie, Systématique et Evolution, UMR8079, CNRS, 91405 Orsay, France
| | - Manuela López-Villavicencio
- Institut de Systématique, Evolution, Biodiversité, UMR 7205 CNRS-MNHN-UPMC-EPHE, Muséum national d'Histoire naturelle, Sorbonne Université, CP39, 57 Rue Cuvier, 75231 Paris Cedex 05, France
| | - Jérôme Gouzy
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, INRA, Castanet-Tolosan 31326, France; Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, CNRS, Castanet-Tolosan 31326, France
| | - Erika Sallet
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, INRA, Castanet-Tolosan 31326, France; Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, CNRS, Castanet-Tolosan 31326, France
| | - Émilie Dumas
- Ecologie, Systématique et Evolution, UMR8079, Univ. Paris-Sud, 91405 Orsay, France; Ecologie, Systématique et Evolution, UMR8079, CNRS, 91405 Orsay, France
| | - Sandrine Lacoste
- Institut de Systématique, Evolution, Biodiversité, UMR 7205 CNRS-MNHN-UPMC-EPHE, Muséum national d'Histoire naturelle, Sorbonne Université, CP39, 57 Rue Cuvier, 75231 Paris Cedex 05, France
| | - Robert Debuchy
- Institut de Génétique et Microbiologie, UMR8621, Univ. Paris-Sud, 91405 Orsay, France; Institut de Génétique et Microbiologie, UMR8621, CNRS, 91405 Orsay, France
| | - Joëlle Dupont
- Institut de Systématique, Evolution, Biodiversité, UMR 7205 CNRS-MNHN-UPMC-EPHE, Muséum national d'Histoire naturelle, Sorbonne Université, CP39, 57 Rue Cuvier, 75231 Paris Cedex 05, France
| | - Antoine Branca
- Ecologie, Systématique et Evolution, UMR8079, Univ. Paris-Sud, 91405 Orsay, France; Ecologie, Systématique et Evolution, UMR8079, CNRS, 91405 Orsay, France.
| | - Tatiana Giraud
- Ecologie, Systématique et Evolution, UMR8079, Univ. Paris-Sud, 91405 Orsay, France; Ecologie, Systématique et Evolution, UMR8079, CNRS, 91405 Orsay, France.
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22
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Murphy HA, Zeyl CW. A Potential Case of Reinforcement in a Facultatively Sexual Unicellular Eukaryote. Am Nat 2015; 186:312-9. [PMID: 26655159 DOI: 10.1086/682071] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
The origin of a new species requires a mechanism to prevent divergent populations from interbreeding. In the classic allopatric model, divided populations evolve independently and accumulate genetic differences. If contact is restored, hybrids suffer reduced fitness and selection may favor traits that prevent mistakes in mating, a process known as reinforcement. This decisive but transient phase is challenging to document and has been reported mostly in macroorganisms. Very little is known about the processes through which new microbial species originate. In particular, it is unclear whether microbial eukaryotes, many of which can reproduce sexually during complex life cycles, speciate in much the same way as do well-studied plants and animals. Using individual cellular mate choice trials, we investigated the mating behavior of sympatric and allopatric woodland populations of the yeast Saccharomyces paradoxus. We find evidence consistent with reinforcement, potentially representing an example of microbial speciation in progress.
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Affiliation(s)
- Helen A Murphy
- Department of Biology, Wake Forest University, Box 7325 Reynolda Station, Winston-Salem, North Carolina 27109
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23
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Pintye A, Ropars J, Harvey N, Shin HD, Leyronas C, Nicot PC, Giraud T, Kiss L. Host phenology and geography as drivers of differentiation in generalist fungal mycoparasites. PLoS One 2015; 10:e0120703. [PMID: 25803832 PMCID: PMC4372539 DOI: 10.1371/journal.pone.0120703] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Accepted: 01/25/2015] [Indexed: 11/19/2022] Open
Abstract
The question as to why parasites remain generalist or become specialist is a key unresolved question in evolutionary biology. Ampelomyces spp., intracellular mycoparasites of powdery mildew fungi, which are themselves plant pathogens, are a useful model for studies of this issue. Ampelomyces is used for the biological control of mildew. Differences in mycohost phenology promote temporal isolation between sympatric Ampelomyces mycoparasites. Apple powdery mildew (APM) causes spring epidemics, whereas other powdery mildew species on plants other than apple cause epidemics later in the season. This has resulted in genetic differentiation between APM and non-APM strains. It is unclear whether there is genetic differentiation between non-APM Ampelomyces lineages due to their specialization on different mycohosts. We used microsatellites to address this question and found no significant differentiation between non-APM Ampelomyces strains from different mycohosts or host plants, but strong differentiation between APM and non-APM strains. A geographical structure was revealed in both groups, with differences between European countries, demonstrating restricted dispersal at the continent scale and a high resolution for our markers. We found footprints of recombination in both groups, possibly more frequent in the APM cluster. Overall, Ampelomyces thus appears to be one of the rare genuine generalist pathogenic fungi able to parasitize multiple hosts in natural populations. It is therefore an excellent model for studying the evolution of pathogens towards a generalist rather than host-specific strategy, particularly in light of the tritrophic interaction between Ampelomyces mycoparasites, their powdery mildew fungal hosts and the mildew host plants.
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Affiliation(s)
- Alexandra Pintye
- Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences (MTA), Budapest, Hungary
| | - Jeanne Ropars
- CNRS (Centre National de la Recherche Scientifique), Ecologie, Systematique et Evolution (ESE), Orsay, France
- Univ Paris Sud, Ecology, Systematique et Evolution (ESE), Orsay, France
| | - Nick Harvey
- Genetic Marker Services, 7 Brighton, United Kingdom
| | - Hyeon-Dong Shin
- Division of Environmental Science and Ecological Engineering, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Christel Leyronas
- Institut National de la Recherche Agronomique (INRA), Unite de Recherche UR407, Unité de Pathologie Végétale, Domaine St. Maurice, Montfavet, France
| | - Philippe C. Nicot
- Institut National de la Recherche Agronomique (INRA), Unite de Recherche UR407, Unité de Pathologie Végétale, Domaine St. Maurice, Montfavet, France
| | - Tatiana Giraud
- CNRS (Centre National de la Recherche Scientifique), Ecologie, Systematique et Evolution (ESE), Orsay, France
- Univ Paris Sud, Ecology, Systematique et Evolution (ESE), Orsay, France
- * E-mail: (TG); (LK)
| | - Levente Kiss
- Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences (MTA), Budapest, Hungary
- * E-mail: (TG); (LK)
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24
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Gladieux P, Feurtey A, Hood ME, Snirc A, Clavel J, Dutech C, Roy M, Giraud T. The population biology of fungal invasions. Mol Ecol 2015; 24:1969-86. [DOI: 10.1111/mec.13028] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 11/24/2014] [Accepted: 11/28/2014] [Indexed: 12/16/2022]
Affiliation(s)
- P. Gladieux
- Ecologie; Systématique et Evolution; Université Paris-Sud; Bâtiment 360 F-91405 Orsay France
- CNRS; 91405 Orsay France
| | - A. Feurtey
- Ecologie; Systématique et Evolution; Université Paris-Sud; Bâtiment 360 F-91405 Orsay France
- CNRS; 91405 Orsay France
| | - M. E. Hood
- Department of Biology; Amherst College; Amherst Massachusetts 01002 USA
| | - A. Snirc
- Ecologie; Systématique et Evolution; Université Paris-Sud; Bâtiment 360 F-91405 Orsay France
- CNRS; 91405 Orsay France
| | - J. Clavel
- Conservation des Espèces; Restauration et Suivi des Populations - CRBPO; Muséum National d'Histoire Naturelle-CNRS-Université Pierre et Marie Curie; 55 rue Buffon 75005 Paris France
| | - C. Dutech
- Biodiversité Gènes et Communautés; INRA-Université Bordeaux 1; Site de Pierroton 33610 Cestas France
| | - M. Roy
- Evolution et Diversité Biologique; Université Toulouse Paul Sabatier-Ecole Nationale de Formation Agronomique-CNRS; 118 route de Narbonne 31062 Toulouse France
| | - T. Giraud
- Ecologie; Systématique et Evolution; Université Paris-Sud; Bâtiment 360 F-91405 Orsay France
- CNRS; 91405 Orsay France
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25
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Gladieux P, Ropars J, Badouin H, Branca A, Aguileta G, Vienne DM, Rodríguez de la Vega RC, Branco S, Giraud T. Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes. Mol Ecol 2014; 23:753-73. [DOI: 10.1111/mec.12631] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 12/04/2013] [Indexed: 12/15/2022]
Affiliation(s)
- Pierre Gladieux
- Ecologie, Systématique et Evolution UMR8079 University of Paris‐Sud Orsay 91405 France
- Ecologie, Systématique et Evolution CNRS UMR8079 Orsay 91405 France
- Department of Plant and Microbial Biology University of California Berkeley CA 94720‐3102 USA
| | - Jeanne Ropars
- Ecologie, Systématique et Evolution UMR8079 University of Paris‐Sud Orsay 91405 France
- Ecologie, Systématique et Evolution CNRS UMR8079 Orsay 91405 France
| | - Hélène Badouin
- Ecologie, Systématique et Evolution UMR8079 University of Paris‐Sud Orsay 91405 France
- Ecologie, Systématique et Evolution CNRS UMR8079 Orsay 91405 France
| | - Antoine Branca
- Ecologie, Systématique et Evolution UMR8079 University of Paris‐Sud Orsay 91405 France
- Ecologie, Systématique et Evolution CNRS UMR8079 Orsay 91405 France
| | - Gabriela Aguileta
- Center for Genomic Regulation (CRG) Dr, Aiguader 88 Barcelona 08003 Spain
- Universitat Pompeu Fabra (UPF) Barcelona 08003 Spain
| | - Damien M. Vienne
- Center for Genomic Regulation (CRG) Dr, Aiguader 88 Barcelona 08003 Spain
- Universitat Pompeu Fabra (UPF) Barcelona 08003 Spain
- Laboratoire de Biométrie et Biologie Evolutive Université Lyon 1 CNRS UMR5558 Villeurbanne 69622 France
| | - Ricardo C. Rodríguez de la Vega
- Ecologie, Systématique et Evolution UMR8079 University of Paris‐Sud Orsay 91405 France
- Ecologie, Systématique et Evolution CNRS UMR8079 Orsay 91405 France
| | - Sara Branco
- Department of Plant and Microbial Biology University of California Berkeley CA 94720‐3102 USA
| | - Tatiana Giraud
- Ecologie, Systématique et Evolution UMR8079 University of Paris‐Sud Orsay 91405 France
- Ecologie, Systématique et Evolution CNRS UMR8079 Orsay 91405 France
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Harder CB, Læssøe T, Frøslev TG, Ekelund F, Rosendahl S, Kjøller R. A three-gene phylogeny of the Mycena pura complex reveals 11 phylogenetic species and shows ITS to be unreliable for species identification. Fungal Biol 2013; 117:764-75. [PMID: 24295915 DOI: 10.1016/j.funbio.2013.09.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Revised: 08/19/2013] [Accepted: 09/20/2013] [Indexed: 11/15/2022]
Abstract
Phylogenetic analyses of Mycena sect. Calodontes using ITS previously suggested ten cryptic monophyletic ITS lineages within the Mycena pura morphospecies. Here, we compare ITS data (645 bp incl. gaps) from 46 different fruit bodies that represent the previously described ITS diversity with partial tEF-1-α (423 bp) and RNA polymerase II (RPB1) (492 bp) sequence data to test the genealogical concordance. While neither of the markers were in complete topological agreement, the branches differing between the tEF and RPB1 trees had a low bootstrap (<50) support, and the partition homogeneity incongruence length difference (ILD) tests were not significant. ILD tests revealed significant discordances between ITS and the tEF and RPB1 markers in several lineages. And our analyses suggested recombination between ITS1 and ITS2, most pronounced in one phylospecies that was identical in tEF and RPB1. Based on the agreement between tEF and RPB1, we defined 11 mutually concordant terminal clades as phylospecies inside the M. pura morphospecies; most of them cryptic. While neither of the markers showed an unequivocal barcoding gap between inter- and intraspecific diversity, the overlap was most pronounced for ITS (intraspecific diversity 0-3.5 %, interspecific diversity 0.4 %-8.8 %). A clustering analysis on tEF separated at a 1.5 % level returned all phylogenetic species as Operational Taxonomic Units (OTUs), while ITS at both a 1.5 % level and at a 3 % threshold level not only underestimated diversity as found by the tEF and RPB1, but also identified an OTU which was not a phylogenetic species. Thus, our investigation does not support the universal suitability of ITS for species recognition in particular, and emphasises the general limitation of single gene analyses combined with single percentage separation values.
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Affiliation(s)
- Christoffer B Harder
- University of Copenhagen, Department of Biology, Terrestrial Ecology, Universitetsparken 15, 2100 København Ø, Denmark.
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Patterns of human oral yeast species distribution on Hainan Island in China. Mycopathologia 2013; 176:359-68. [PMID: 24085613 DOI: 10.1007/s11046-013-9703-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 09/09/2013] [Indexed: 10/26/2022]
Abstract
Infections by yeast strains of the genus Candida are among the most prevalent fungal infections of humans. These yeasts are common residents of the oral mucosa and other body surfaces. Since most yeast infections are due to endogenous strains and that species of Candida differ in virulence properties and in intrinsic susceptibilities to antifungal drugs, understanding the human commensal yeast flora can help designing effective treatment and prevention strategies against yeast infections. Here, we report the patterns of yeast species distributions in the oral cavities of 1,799 people from Hainan Island in southern China. Based on sequence information at the fungal barcode locus ITS regions, 368 of the 415 obtained oral yeast strains were identified as belonging to 26 yeast species, while the remaining 47 strains all showed significant sequence divergence to the currently described species. The four most common yeast species were C. albicans (42 %), C. tropicalis (20 %), C. glabrata (5.5 %), and C. parapsilosis (4.1 %) and 10 of the 26 yeast species were represented by only one strain each. Our analyses identified that the gender of hosts and ethnical background showed no contribution to oral yeast species distributions. However, the health status, place of birth, current residency, and the age of hosts all showed significant contributions to the distributions of the four dominant yeast species. We compared our results with those reported previously and discussed the potential mechanisms for the observed differences in oral yeast species distributions.
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Hughes KW, Petersen RH, Lodge DJ, Bergemann SE, Baumgartner K, Tulloss RE, Lickey E, Cifuentes J. Evolutionary consequences of putative intra-and interspecific hybridization in agaric fungi. Mycologia 2013; 105:1577-94. [PMID: 23928423 DOI: 10.3852/13-041] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Agaric fungi of the southern Appalachian Mountains including Great Smoky Mountains National Park are often heterozygous for the rDNA internal transcribed spacer region (ITS) with >42% of collections showing some heterozygosity for indels and/or base-pair substitutions. For these collections, intra-individual haplotype divergence is typically less than 2%, but for 3% of these collections intra-individual haplotype divergence exceeds that figure. We hypothesize that high intra-individual haplotype divergence is due to hybridization between agaric fungi with divergent haplotypes, possibly migrants from geographically isolated glacial refugia. Four species with relatively high haplotype divergence were examined: Armillaria mellea, Amanita citrina f. lavendula, Gymnopus dichrous and the Hygrocybe flavescens/chlorophana complex. The ITS region was sequenced, haplotypes of heterozygotes were resolved through cloning, and phylogenetic analyses were used to determine the outcome of hybridization events. Within Armillaria mellea and Amanita citrina f. lavendula, we found evidence of interbreeding and recombination. Within G. dichrous and H. flavescens/chlorophana, hybrids were identified but there was no evidence for F2 or higher progeny in natural populations suggesting that the hybrid fruitbodies might be an evolutionary dead end and that the genetically divergent Mendelian populations from which they were derived are, in fact, different species. The association between ITS haplotype divergence of less than 5% (Armillaria mellea = 2.6% excluding gaps; Amanita citrina f. lavendula = 3.3%) with the presence of putative recombinants and greater than 5% (Gymnopus dichrous = 5.7%; Hygrocybe flavescens/chlorophana = 14.1%) with apparent failure of F1 hybrids to produce F2 or higher progeny in populations may suggest a correlation between genetic distance and reproductive isolation.
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Affiliation(s)
- Karen W Hughes
- Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee 37996-1100
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de Vienne DM, Refrégier G, López-Villavicencio M, Tellier A, Hood ME, Giraud T. Cospeciation vs host-shift speciation: methods for testing, evidence from natural associations and relation to coevolution. THE NEW PHYTOLOGIST 2013; 198:347-385. [PMID: 23437795 DOI: 10.1111/nph.12150] [Citation(s) in RCA: 259] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 12/19/2012] [Indexed: 05/26/2023]
Abstract
Hosts and their symbionts are involved in intimate physiological and ecological interactions. The impact of these interactions on the evolution of each partner depends on the time-scale considered. Short-term dynamics - 'coevolution' in the narrow sense - has been reviewed elsewhere. We focus here on the long-term evolutionary dynamics of cospeciation and speciation following host shifts. Whether hosts and their symbionts speciate in parallel, by cospeciation, or through host shifts, is a key issue in host-symbiont evolution. In this review, we first outline approaches to compare divergence between pairwise associated groups of species, their advantages and pitfalls. We then consider recent insights into the long-term evolution of host-parasite and host-mutualist associations by critically reviewing the literature. We show that convincing cases of cospeciation are rare (7%) and that cophylogenetic methods overestimate the occurrence of such events. Finally, we examine the relationships between short-term coevolutionary dynamics and long-term patterns of diversification in host-symbiont associations. We review theoretical and experimental studies showing that short-term dynamics can foster parasite specialization, but that these events can occur following host shifts and do not necessarily involve cospeciation. Overall, there is now substantial evidence to suggest that coevolutionary dynamics of hosts and parasites do not favor long-term cospeciation.
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Affiliation(s)
- D M de Vienne
- Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - G Refrégier
- Université Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, 91405, Orsay, France
- CNRS, UMR8621, 91405, Orsay, France
| | - M López-Villavicencio
- Muséum National d'Histoire Naturelle, 57 rue Cuvier, F-75231, Paris Cedex 05, France
| | - A Tellier
- Section of Population Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, D-85354, Freising, Germany
| | - M E Hood
- Department of Biology, Amherst College, Amherst, MA, USA
| | - T Giraud
- Université Paris-Sud, Ecologie, Systématique et Evolution, UMR 8079, 91405, Orsay, France
- CNRS, UMR8079, 91405, Orsay, France
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30
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Lambert SM, Geneva AJ, Luke Mahler D, Glor RE. Using genomic data to revisit an early example of reproductive character displacement in HaitianAnolislizards. Mol Ecol 2013; 22:3981-95. [DOI: 10.1111/mec.12292] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Revised: 02/12/2013] [Accepted: 02/14/2013] [Indexed: 12/14/2022]
Affiliation(s)
- Shea M. Lambert
- University of Arizona; Tucson AZ 85721 USA
- University of Rochester; Rochester NY 14627 USA
| | | | - D. Luke Mahler
- Center for Population Biology; University of California; Davis CA 95616 USA
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Hollander J, Smadja CM, Butlin RK, Reid DG. Genital divergence in sympatric sister snails. J Evol Biol 2012; 26:210-5. [DOI: 10.1111/jeb.12029] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Revised: 09/24/2012] [Accepted: 09/24/2012] [Indexed: 11/30/2022]
Affiliation(s)
- J. Hollander
- Department of Biology, Aquatic Ecology; Lund University; Lund Sweden
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield UK
| | - C. M. Smadja
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield UK
- Centre National de la Recherche Scientifique (CNRS); Institut des Sciences de l'Evolution UMR 5554; Montpellier France
| | - R. K. Butlin
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield UK
| | - D. G. Reid
- Department of Life Sciences; Natural History Museum; London UK
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Abstract
Reproductive isolation is an essential ingredient of speciation, and much has been learned in recent years about the evolution of reproductive isolation and the genetics of reproductive barriers in animals and plants. Fungi have been neglected on these aspects, despite being tractable model eukaryotes. Here, we used a model fitting approach to look at the importance of different barriers to gene flow to explain the decrease of reproductive compatibility with genetic distance in fungi. We found support for the occurrence of reinforcement in the presyngamy compatibility among basidiomycetes. In contrast, no evidence for reinforcement was detected in ascomycetes, concurring with the idea that host/habitat adaptation in this group can pleiotropically cause reproductive isolation. We found no evidence of a snowballing accumulation of postsyngamic reproductive incompatibilities in either ascomycetes or the complex of anther smut fungi. Together with previous studies, our results suggest that ecologically based barriers to gene flow and karyotypic differences may have an important role in hybrid inviability and sterility in fungi. Interestingly, hybrid sterility appeared to evolve faster than hybrid inviability in fungi.
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Jewell C, Papineau AD, Freyre R, Moyle LC. Patterns of reproductive isolation in Nolana (Chilean bellflower). Evolution 2012; 66:2628-36. [PMID: 22834759 DOI: 10.1111/j.1558-5646.2012.01607.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We examined reproductive isolating barriers at four postmating stages among 11 species from the morphologically diverse genus Nolana (Solanaceae). At least one stage was positively correlated with both genetic and geographic distance between species. Postzygotic isolation was generally stronger and faster evolving than postmating prezygotic isolation. In addition, there was no evidence for mechanical isolation, or for reproductive character displacement in floral traits that can influence pollinator isolation. In general, among the potential isolating stages examined here, postzygotic barriers appear to be more effective contributors to reducing gene flow, including between sympatric species.
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Affiliation(s)
- Cathleen Jewell
- Department of Biology, Indiana University, Bloomington, Indiana 47408, USA
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35
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Gibson AK, Hood ME, Giraud T. Sibling competition arena: selfing and a competition arena can combine to constitute a barrier to gene flow in sympatry. Evolution 2012; 66:1917-30. [PMID: 22671556 DOI: 10.1111/j.1558-5646.2011.01563.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Closely related species coexisting in sympatry provide critical insight into the mechanisms underlying speciation and the maintenance of genetic divergence. Selfing may promote reproductive isolation by facilitating local adaptation, causing reduced hybrid fitness in parental environments. Here, we propose a novel mechanism by which selfing can further impair interspecific gene flow: selfing may act to ensure that nonhybrid progeny systematically co-occur whenever hybrid genotypes are produced. Under a competition arena, the fitness differentials between nonhybrid and hybrid progeny are then magnified, preventing development of interspecific hybrids. We investigate whether this "sibling competition arena" can explain the coexistence in sympatry of closely related species of the plant fungal pathogens (Microbotryum) causing anther-smut disease. The probabilities of intrapromycelial mating (automixis), outcrossing, and sibling competition were manipulated in artificial inoculations to evaluate their contribution to reproductive isolation. We report that both intrapromycelial selfing and sibling competition significantly reduced rates of hybrid infection beyond that expected based solely upon selfing rates and noncompetitive fitness differentials between hybrid and nonhybrid progeny. Our results thus suggest that selfing and a sibling competition arena can combine to constitute a barrier to gene flow and diminish selection for additional barriers to gene flow in sympatry.
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Affiliation(s)
- A K Gibson
- Laboratoire Ecologie, Systématique et Evolution, Université Paris Sud, 91405 Orsay, France.
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36
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Murphy HA, Zeyl CW. PREZYGOTIC ISOLATION BETWEEN SACCHAROMYCES CEREVISIAE AND SACCHAROMYCES PARADOXUS THROUGH DIFFERENCES IN MATING SPEED AND GERMINATION TIMING. Evolution 2011; 66:1196-209. [DOI: 10.1111/j.1558-5646.2011.01516.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Walker AS, Gautier AL, Confais J, Martinho D, Viaud M, Le P Cheur P, Dupont J, Fournier E. Botrytis pseudocinerea, a new cryptic species causing gray mold in French vineyards in sympatry with Botrytis cinerea. PHYTOPATHOLOGY 2011; 101:1433-45. [PMID: 21830954 DOI: 10.1094/phyto-04-11-0104] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Botrytis cinerea is a major crop pathogen infesting >220 hosts worldwide. A cryptic species has been identified in some French populations but the new species, B. pseudocinerea, has not been fully delimited and established. The aim of this study was to distinguish between the two species, using phylogenetic, biological, morphological, and ecological criteria. Multiple gene genealogies confirmed that the two species belonged to different, well-supported phylogenetic clades. None of the morphological criteria tested (spore size, germination rate, or mycelial growth) was able to discriminate between these two species. Sexual crosses between individuals from the same species and different species were carried out. Only crosses between individuals from the same species were successful. Moreover, population genetics analysis revealed a high level of diversity within each species and a lack of gene flow between them. Finally, a population survey over time showed that B. cinerea was the predominant species but that B. pseudocinerea was more abundant in spring, on floral debris. This observation could not be explained by temperature adaptation in tests carried out in vitro or by aggressiveness on tomato or bean leaves. This study clearly establishes that B. cinerea and B. pseudocinerea constitute a complex of two cryptic species living in sympatry on several hosts, including grapevine and blackberry. We propose several biological or molecular tools for unambiguous differentiation between the two species. B. pseudocinerea probably makes a negligible contribution to gray mold epidemics on grapevine. This new species has been deposited in the MycoBank international database.
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GLADIEUX PIERRE, GUÉRIN FABIEN, GIRAUD TATIANA, CAFFIER VALÉRIE, LEMAIRE CHRISTOPHE, PARISI LUCIANA, DIDELOT FRÉDÉRIQUE, LE CAM BRUNO. Emergence of novel fungal pathogens by ecological speciation: importance of the reduced viability of immigrants. Mol Ecol 2011; 20:4521-32. [DOI: 10.1111/j.1365-294x.2011.05288.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Genetic architecture of a reinforced, postmating, reproductive isolation barrier between Neurospora species indicates evolution via natural selection. PLoS Genet 2011; 7:e1002204. [PMID: 21876674 PMCID: PMC3158040 DOI: 10.1371/journal.pgen.1002204] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Accepted: 06/10/2011] [Indexed: 11/20/2022] Open
Abstract
A role for natural selection in reinforcing premating barriers is recognized, but selection for reinforcement of postmating barriers remains controversial. Organisms lacking evolvable premating barriers can theoretically reinforce postmating isolation, but only under restrictive conditions: parental investment in hybrid progeny must inhibit subsequent reproduction, and selected postmating barriers must restore parents' capacity to reproduce successfully. We show that reinforced postmating isolation markedly increases maternal fitness in the fungus Neurospora crassa, and we detect the evolutionary genetic signature of natural selection by quantitative trait locus (QTL) analysis of the reinforced barrier. Hybrid progeny of N. crassa and N. intermedia are highly inviable. Fertilization by local N. intermedia results in early abortion of hybrid fruitbodies, and we show that abortion is adaptive because only aborted maternal colonies remain fully receptive to future reproduction. In the first QTL analysis of postmating reinforcement in microbial eukaryotes, we identify 11 loci for abortive hybrid fruitbody development, including three major QTLs that together explain 30% of trait variance. One of the major QTLs and six QTLs of lesser effect are found on the mating-type determining chromosome of Neurospora. Several reinforcement QTLs are flanked by genetic markers showing either segregation distortion or non-random associations with alleles at other loci in a cross between N. crassa of different clades, suggesting that the loci also are associated with local effects on same-species reproduction. Statistical analysis of the allelic effects distribution for abortive hybrid fruitbody development indicates its evolution occurred under positive selection. Our results strongly support a role for natural selection in the evolution of reinforced postmating isolation in N. crassa. Although Darwin believed that natural selection could not drive intersterility between species, it is now well established that there is a role for natural selection in the evolution of premating discrimination that reinforces barriers to hybridization. However, natural selection for postmating barriers, like hybrid inviability, is still controversial, because it can only occur when overall maternal fitness is increased by the inviability of hybrid offspring. Constraint on adaptive evolution of postmating barriers poses a problem when organisms without premating preferences must adapt to the presence of related species and ensure that reproduction occurs only between members of the same species. We studied the evolutionary genetics of a reinforced, postmating barrier between two species of mold, Neurospora crassa and N. intermedia. Although hybrids have low fitness, Neurospora females do not discriminate against different-species sex partners before mating. Instead, N. crassa has adapted to the presence of the N. intermedia in its range by selectively aborting hybrid fruitbodies. We show that abortion increases maternal fitness because N. crassa can mate again after hybridization only if fruitbodies abort. Abortion is controlled by 11 loci, whose genetic effects are consistent with an adaptive evolution model, confirming that abortion evolved via natural selection against hybridization.
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Cai L, Giraud T, Zhang N, Begerow D, Cai G, Shivas RG. The evolution of species concepts and species recognition criteria in plant pathogenic fungi. FUNGAL DIVERS 2011. [DOI: 10.1007/s13225-011-0127-8] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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41
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Abstract
Sympatric sister species are predicted to have greater divergence in reproductive traits than allopatric sister species, especially if mating system shifts, such as the evolution of self-fertilization, are more likely to originate within the geographic range of the outcrossing ancestor. We present evidence that supports this expectation-sympatric sister species in the monkeyflower genus, Mimulus, exhibit greater divergence in flower size than allopatric sister species. Additionally, we find that sympatric sister species are more likely to have one species with anthers that overtop their stigmas than allopatric sister species, suggesting that the evolution of automatic self-pollination may contribute to this pattern. Potential mechanisms underlying this pattern include reinforcement and a stepping stone model of parapatric speciation.
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Affiliation(s)
- Dena L Grossenbacher
- Department of Evolution and Ecology, University of California, Davis, California 95616, USA.
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42
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Bultman TL, Leuchtmann A, Sullivan TJ, Dreyer AP. Do Botanophila flies provide reproductive isolation between two species of Epichloë fungi? A field test. THE NEW PHYTOLOGIST 2011; 190:206-212. [PMID: 21244433 DOI: 10.1111/j.1469-8137.2010.03612.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Epichloë spp., fungal endophytes of cool season grasses, produce collars of mycelium (stromata) on host stems that Botanophila flies visit for egg laying. Flies transfer fungal gametes among stromata and thereby serve to cross-fertilize fungi. Hence, the interaction is analogous to insect pollination in angiosperms. While most Epichloë species are not interfertile, Epichloë typhina and Epichloë clarkii can hybridize. We investigated whether Botanophila flies play a role in the reproductive isolation of the two Epichloë species at a field site in southwestern Switzerland. We estimated the density of stromata and collected fly larvae and stromata occurring on plants. While most ascospores collected from both species indicated intraspecific mating, 9.3% of fungal fruiting bodies contained spores of hybrid origin. Two species of Botanophila larvae occurred on stromata and both preferred E. typhina. Yet, both fly species laid eggs on both fungal species. While preferences by Botanophila flies should influence reproductive isolation between the fungi, other mechanisms are likely more important. Our data, which show hybrid ascospores are produced, suggest postzygotic isolating mechanisms are an important means of reproductive isolation.
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Affiliation(s)
| | - Adrian Leuchtmann
- Plant Ecological Genetics, Institute of Integrative Biology, ETH Zürich, Universitätstrasse 16, CH-8092 Zürich, Switzerland
| | - T J Sullivan
- Biology Department, Hope College, Holland, MI 49423, USA
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Kiss L, Pintye A, Kovács GM, Jankovics T, Fontaine MC, Harvey N, Xu X, Nicot PC, Bardin M, Shykoff JA, Giraud T. Temporal isolation explains host-related genetic differentiation in a group of widespread mycoparasitic fungi. Mol Ecol 2011; 20:1492-507. [PMID: 21261766 DOI: 10.1111/j.1365-294x.2011.05007.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Understanding the mechanisms responsible for divergence and specialization of pathogens on different hosts is of fundamental importance, especially in the context of the emergence of new diseases via host shifts. Temporal isolation has been reported in a few plants and parasites, but is probably one of the least studied speciation processes. We studied whether temporal isolation could be responsible for the maintenance of genetic differentiation among sympatric populations of Ampelomyces, widespread intracellular mycoparasites of powdery mildew fungi, themselves plant pathogens. The timing of transmission of Ampelomyces depends on the life cycles of the powdery mildew species they parasitize. Internal transcribed spacer sequences and microsatellite markers showed that Ampelomyces populations found in apple powdery mildew (Podosphaera leucotricha) were genetically highly differentiated from other Ampelomyces populations sampled from several other powdery mildew species across Europe, infecting plant hosts other than apple. While P. leucotricha starts its life cycle early in spring, and the main apple powdery mildew epidemics occur before summer, the fungal hosts of the other Ampelomyces cause epidemics mainly in summer and autumn. When two powdery mildew species were experimentally exposed to Ampelomyces strains naturally occurring in P. leucotricha in spring, and to strains naturally present in other mycohost species in autumn, cross-infections always occurred. Thus, the host-related genetic differentiation in Ampelomyces cannot be explained by narrow physiological specialization, because Ampelomyces were able to infect powdery mildew species they were unlikely to have encountered in nature, but instead appears to result from temporal isolation.
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Affiliation(s)
- Levente Kiss
- Plant Protection Institute of the Hungarian Academy of Sciences, Budapest, Hungary.
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Nydam ML, Harrison RG. Reproductive protein evolution in two cryptic species of marine chordate. BMC Evol Biol 2011; 11:18. [PMID: 21247489 PMCID: PMC3036616 DOI: 10.1186/1471-2148-11-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Accepted: 01/19/2011] [Indexed: 12/11/2022] Open
Abstract
Background Reproductive character displacement (RCD) is a common and taxonomically widespread pattern. In marine broadcast spawning organisms, behavioral and mechanical isolation are absent and prezygotic barriers between species often operate only during the fertilization process. Such barriers are usually a consequence of differences in the way in which sperm and egg proteins interact, so RCD can be manifest as faster evolution of these proteins between species in sympatry than allopatry. Rapid evolution of these proteins often appears to be a consequence of positive (directional) selection. Here, we identify a set of candidate gamete recognition proteins (GRPs) in the ascidian Ciona intestinalis and showed that these GRPs evolve more rapidly than control proteins (those not involved in gamete recognition). Choosing a subset of these gamete recognition proteins that show evidence of positive selection (CIPRO37.40.1, CIPRO60.5.1, CIPRO100.7.1), we then directly test the RCD hypothesis by comparing divergence (omega) and polymorphism (McDonald-Kreitman, Tajima's D, Fu and Li's D and F, Fay and Wu's H) statistics in sympatric and allopatric populations of two distinct forms of C. intestinalis (Types A and B) between which there are strong post-zygotic barriers. Results Candidate gamete recognition proteins from two lineages of C. intestinalis (Type A and B) are evolving more rapidly than control proteins, consistent with patterns seen in insects and mammals. However, ω (dN/dS) is not significantly different between the sympatric and allopatric populations, and none of the polymorphism statistics show significant differences between sympatric and allopatric populations. Conclusions Enhanced prezygotic isolation in sympatry has become a well-known feature of gamete recognition proteins in marine broadcast spawners. But in most cases the evolutionary process or processes responsible for this pattern have not been identified. Although gamete recognition proteins in C. intestinalis do appear to evolve more rapidly, on average, than proteins with other functions, rates of evolution are not different in allopatric and sympatric populations of the two reproductively isolated forms. That sympatry is probably human-mediated, and therefore recent, may explain the absence of RCD.
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Affiliation(s)
- Marie L Nydam
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York 14853, USA.
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Turner E, Jacobson DJ, Taylor JW. Reinforced postmating reproductive isolation barriers in Neurospora, an Ascomycete microfungus. J Evol Biol 2010; 23:1642-56. [PMID: 20546092 DOI: 10.1111/j.1420-9101.2010.02030.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Maladaptive hybridization promotes reinforcement, selection for stringent reproductive isolation barriers during speciation. Reinforcement is suspected when barriers between sympatric populations are stronger than allopatric barriers, and particularly when stronger barriers evolve in the species and sex suffering the greatest costs of hybridization. Canonically, reinforcement involves premating barriers. Selection for postmating barriers is controversial, but theoretically possible. We examined geographical patterns in reproductive isolation barriers between Neurospora crassa and Neurospora intermedia, fungi with pheromone-mediated mate recognition and maternal care. We find that isolation is stronger between sympatric populations than allopatric populations, and stronger barriers are associated with the species (N. crassa) and mating role (maternal) suffering the greater costs of hybridization. Notably, reinforced isolation involves a postmating barrier, abortion of fruitbodies. We hypothesize that fruitbody abortion is selectively advantageous if it increases the likelihood that maternal Neurospora individuals successfully mate conspecifically after maladaptive hybrid fertilization.
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Affiliation(s)
- E Turner
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94709, USA.
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Giraud T, Gladieux P, Gavrilets S. Linking the emergence of fungal plant diseases with ecological speciation. Trends Ecol Evol 2010; 25:387-95. [PMID: 20434790 DOI: 10.1016/j.tree.2010.03.006] [Citation(s) in RCA: 198] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Revised: 03/27/2010] [Accepted: 03/30/2010] [Indexed: 11/18/2022]
Abstract
Emerging diseases represent a growing worldwide problem accompanying global environmental changes. There is tremendous interest in identifying the factors controlling the appearance and spread of these diseases. Here, we discuss emerging fungal plant diseases, and argue that they often result from host shift speciation (a particular case of ecological speciation). We consider the factors controlling local adaptation and ecological speciation, and show that certain life-history traits of many fungal plant pathogens are conducive for rapid ecological speciation, thus favoring the emergence of novel pathogen species adapted to new hosts. We argue that placing the problem of emerging fungal diseases of plants within the context of ecological speciation can significantly improve our understanding of the biological mechanisms governing the emergence of such diseases.
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Affiliation(s)
- Tatiana Giraud
- Ecologie, Systematique et Evolution, Universite Paris-Sud, 92120 Orsay, France
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Geyer LB, Lessios H. Lack of Character Displacement in the Male Recognition Molecule, Bindin, in Altantic Sea Urchins of the Genus Echinometra. Mol Biol Evol 2009; 26:2135-46. [DOI: 10.1093/molbev/msp122] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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Multiple gene genealogies and phenotypic data reveal cryptic species of the Botryosphaeriaceae: A case study on the Neofusicoccum parvum/N. ribis complex. Mol Phylogenet Evol 2009; 51:259-68. [DOI: 10.1016/j.ympev.2008.12.017] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2008] [Revised: 12/05/2008] [Accepted: 12/16/2008] [Indexed: 11/20/2022]
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De Vienne DM, Refrégier G, Hood ME, Guigue A, Devier B, Vercken E, Smadja C, Deseille A, Giraud T. Hybrid sterility and inviability in the parasitic fungal species complex Microbotryum. J Evol Biol 2009; 22:683-98. [PMID: 19228274 DOI: 10.1111/j.1420-9101.2009.01702.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Microbotryum violaceum, the anther-smut fungus, forms a complex of sibling species which specialize on different plants. Previous studies have shown the presence of partial ecological isolation and F1 inviability, but did not detect assortative mating apart from a high selfing rate. We investigated other post-mating barriers and show that F1 hybrid sterility, the inability of gametes to mate, increased gradually with the increasing genetic distance between the parents. F2 hybrids showed a reduced ability to infect the plants that was also correlated with the genetic distance. The host on which the F2 hybrids were passaged caused a selection for alleles derived from the pathogen species originally isolated from that host, but this effect was not detectable for the most closely related species. The post-mating barriers thus remain weak among the closest species pairs, suggesting that premating barriers are sufficient to initiate divergence in this system.
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Affiliation(s)
- D M De Vienne
- Ecologie, Systématique et Evolution, Université Paris-Sud, Orsay Cedex, France
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Karchani-Balma S, Gautier A, Raies A, Fournier E. Geography, plants, and growing systems shape the genetic structure of Tunisian Botrytis cinerea populations. PHYTOPATHOLOGY 2008; 98:1271-1279. [PMID: 19000001 DOI: 10.1094/phyto-98-12-1271] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Botrytis cinerea, considered for a long time as a generalist fungal pathogen of a multitude of plants, was recently shown to exhibit significant population structure in France according to the host, suggesting sympatric specialization. Recent models also showed that adaptation to new hosts may facilitate the process of sympatric speciation in fungal plant pathogens. The present work aimed at investigating if host plants, combined with geographic origin and growing systems, shape the diversity and structure of Tunisian populations of B. cinerea. We genotyped 153 isolates with 9 microsatellites. In all the investigated populations, the fungus reproduced mainly sexually. Gene flow was significantly reduced between greenhouses and open fields from strawberry but not from grapevine. Populations from tomatoes, sampled under greenhouses only, exhibited a low genotypic diversity. The effects of plant and geography from open fields were investigated on a sample of 74 isolates. Six populations were inferred, mainly structured according to a geographic barrier corresponding to the Grande Dorsale Mountain. However, this effect could not be separated from the host plant origin of isolates. The analysis of 63 isolates recovered from strawberries and faba beans in the Cap Bon and Centre regions did not reveal any significant effect of plant on pathogen population differentiation.
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Affiliation(s)
- S Karchani-Balma
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Campus Universitaire, Tunisie
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